12-109085025-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032663.5(USP30):c.1241C>T(p.Thr414Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000386 in 1,605,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T414A) has been classified as Uncertain significance.
Frequency
Consequence
NM_032663.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP30 | NM_032663.5 | c.1241C>T | p.Thr414Met | missense_variant | 12/13 | ENST00000257548.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP30 | ENST00000257548.10 | c.1241C>T | p.Thr414Met | missense_variant | 12/13 | 1 | NM_032663.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000403 AC: 10AN: 248224Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134320
GnomAD4 exome AF: 0.0000330 AC: 48AN: 1453450Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 22AN XY: 722892
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2022 | The c.1241C>T (p.T414M) alteration is located in exon 12 (coding exon 12) of the USP30 gene. This alteration results from a C to T substitution at nucleotide position 1241, causing the threonine (T) at amino acid position 414 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at